The problem of disambiguating a participle that is part of a verb phrase from a participle that is an adjective is not related at all to the past perfect tense. Any time you have the verb
to be in any tense, the same problem can occur.
You seem to be focusing on present participles.
As a general rule -- but it is not 100% accurate -- an animate subject will lead you to think of the -ing word as part of a verb phrase. (That's the case with both of your examples.)
An inanimate subject is often a signal that the -ing word is an adjective. The present participle in the latter case is often from a verb of psychological state -- a word that expresses a human reaction to a situation.
Examples of present participles as adjectives: amusing, annoying, confusing, disgusting, embarrassing, exciting, horrifying, irritating, maddening, perplexing, revolting, sickening, surprising, troubling, upsetting.
The play [is / was / had been / will be / ... ] [amusing / exciting / perplexing].
The food [is / was / had been / will be / ... ] [disgusting / sickening].
The sight of all that blood [is / was / ...] [horrifying / troubling].
The present participles of some of these verbs are occasionally used as parts of verb phrases with human beings as direct objects:
The yapping dogs [are / have been] [annoying / upsetting] your mother. Take them outside.
Her unusual behavior was clearly [embarrassing / irritating] the guests.
Peter [is / was] always surprising his wife with expensive gifts.
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Note how the presence of a direct object makes the participle part of a verb phrase:
His actions were embarrassing. (were embarrassing : linking verb and adjective)
His actions were embarrassing the women. (were embarrassing : verb phrase)
CJ